Do you think it's possible he uncovered actual special access black project programs that the congress is not being properly informed about and which are not receiving the kind of oversight that is legally required?
. . .
But another possibility is that retaliation could be taking place because he's stumbled upon something worth blowing the whistle on that is not alien-related even though he thinks it is. And retaliation would make sense against him to keep the lid closed on whatever he's actually stumbled upon.
I can only answer from my experience of serving a modern military organization with a personnel strength of hundreds of thousands which is sizeable yet much smaller than the armed forces of the US.
The bedrock of a modern, legally mandated, defence organization is its underlying ethos of
protecting civilians from armed aggression. The military code and honour of being a protector/defender, rather than a harrasser/retaliator, of civilians
irrespective of who they are, runs deep and is not mere lip-service whereby we polish the veneer of an establishment which is actually rotten to the core or rife with corruption. In fact, we're relatively free from a particular scourge which sometimes plagues the police force -- namely the tendency to regard the civilian population with a certain degree of cynicism whereby every type of group produces a percentage of convicted felons despite the appearance of innocence. For the military, they're all just nice little sheep to be fenced in and guarded, and whatever else failings they have do not concern us. We'll leave it for the police and other civilian authorities.
Sure, we're all humans and you're bound to find individuals, especially in huge establishments, that are not only unethical but veritably commit crimes for which they have to face legal consequences. But overall, the rank and file of a defence organization has a kind of an adult and professional version of a boyscout culture that runs across all compartments, branches and military disciplines, with many compartment-specific (and sometimes highly peculiar and even amusing) sub-cultures such as that of the Air Force, Navy, various special operations commands, the Marine Corps, etc.
Only a sinister and unprofessional organization, used to operating outside the purview of law, would conspire to persecute and retaliate "whistleblowers" rather than pursue legal means openly, robustly and professionally. I find it very hard to believe that the DoD is genuinely as sinister as painted by, yes, conspiracy theorists. At worst, certain individuals with an axe to grind with Grusch could have taken matters in their own hand. But if so, it's highly dishonourable as it's both unethical and since taking matters in your own hand runs counter to the very soul, the very core training, of what it means to be a soldier.
So that's my long-winded answer.
However, I do think it's very possible that the DoD has a whole category of highly classified information, maybe even a few extra-sensitive programs, the knowledge of which needs to be withheld even from Congress 'oversight' by invoking the President's executive privilege if all else fails. This type of 'check and balance', whereby the President isn't
fully subservient to the 'elected representatives', serves the interest of the people simply due to the
higher risk of leakage from politicians as opposed to duty-bound officers observing single-mindedly an honour code and their assigned duties under law. The Members of Congress are ultimately public figures more bent on votes than on duty to uphold national security secrets whose reasons of classification they might (1) not fully understand or (2) agree with in their sometimes arrogant presumption of greater intelligence and judgment as America's elected leaders. If there weren't any trust issues on critical details of sensitive capabilities leaking, if only out of the unintentional sloppiness of politicians, to the public and, by extension, to the adversarsies, such an executive privilege wouldn't perhaps be necessary.
P.S. Whilst the option that Grusch got
actually retaliated by the DoD for snooping around non-alien classified programs is far likelier than retaliations for exposing alien secrets, it's still far unlikelier than the main hypothesis of ufologists snooping around
beyond their need-to-know within the Pentagon and becoming overly paranoid and angered after being rightfully denied access in the interest of national security.